Logging started at 12:59:32 on 15 Sep 2015
QIIME version: 1.9.1

qiime_config values:
pick_otus_reference_seqs_fp	/usr/local/lib/python2.7/dist-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta
sc_queue	all.q
pynast_template_alignment_fp	/usr/local/lib/python2.7/dist-packages/qiime_default_reference/gg_13_8_otus/rep_set_aligned/85_otus.pynast.fasta
cluster_jobs_fp	start_parallel_jobs.py
assign_taxonomy_reference_seqs_fp	/usr/local/lib/python2.7/dist-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta
torque_queue	friendlyq
jobs_to_start	1
denoiser_min_per_core	50
assign_taxonomy_id_to_taxonomy_fp	/usr/local/lib/python2.7/dist-packages/qiime_default_reference/gg_13_8_otus/taxonomy/97_otu_taxonomy.txt
temp_dir	/tmp/
blastall_fp	blastall
seconds_to_sleep	1

parameter file values:
parallel:jobs_to_start	1

Input file md5 sums:
filtered-table.even1000.biom: 269451a2fe65b0ab6072abca4e91f81d
map.tsv: f59d06b2c7b7ae60f51b6fa43100ec95
closed-ref/97_otus.tree: b7e76593bce82913af1cfb06edf15732

Executing commands.

# Beta Diversity (weighted_unifrac) command 
beta_diversity.py -i filtered-table.even1000.biom -o beta --metrics weighted_unifrac  -t closed-ref/97_otus.tree 

Stdout:

Stderr:

# Rename distance matrix (weighted_unifrac) command 
mv beta/weighted_unifrac_filtered-table.even1000.txt beta/weighted_unifrac_dm.txt

Stdout:

Stderr:

# Principal coordinates (weighted_unifrac) command 
principal_coordinates.py -i beta/weighted_unifrac_dm.txt -o beta/weighted_unifrac_pc.txt 

Stdout:

Stderr:
/usr/local/lib/python2.7/dist-packages/skbio/stats/ordination/_principal_coordinate_analysis.py:107: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it's probably safe to ignore them, but if they are large in magnitude, the results won't be useful. See the Notes section for more details. The smallest eigenvalue is -0.0383198476761 and the largest is 5.40236720685.
  RuntimeWarning

# Make emperor plots, weighted_unifrac) command 
make_emperor.py -i beta/weighted_unifrac_pc.txt -o beta/weighted_unifrac_emperor_pcoa_plot/ -m map.tsv 

Stdout:

Stderr:

# Beta Diversity (unweighted_unifrac) command 
beta_diversity.py -i filtered-table.even1000.biom -o beta --metrics unweighted_unifrac  -t closed-ref/97_otus.tree 

Stdout:

Stderr:

# Rename distance matrix (unweighted_unifrac) command 
mv beta/unweighted_unifrac_filtered-table.even1000.txt beta/unweighted_unifrac_dm.txt

Stdout:

Stderr:

# Principal coordinates (unweighted_unifrac) command 
principal_coordinates.py -i beta/unweighted_unifrac_dm.txt -o beta/unweighted_unifrac_pc.txt 

Stdout:

Stderr:
/usr/local/lib/python2.7/dist-packages/skbio/stats/ordination/_principal_coordinate_analysis.py:107: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it's probably safe to ignore them, but if they are large in magnitude, the results won't be useful. See the Notes section for more details. The smallest eigenvalue is -0.00123991437198 and the largest is 2.97184322851.
  RuntimeWarning

# Make emperor plots, unweighted_unifrac) command 
make_emperor.py -i beta/unweighted_unifrac_pc.txt -o beta/unweighted_unifrac_emperor_pcoa_plot/ -m map.tsv 

Stdout:

Stderr:


Logging stopped at 12:59:53 on 15 Sep 2015
